Welcome to VEnCode’s documentation!

Contents:

• Getting Started
  • Prerequisites
  • Installing
  • Using the module
  • Running the Tests
  • Contributing
  • Versioning
  • Authors
  • License
  • Acknowledgements
• Main Tools
  • Preparing the data
    • Objects for general data
    • Objects for FANTOM5 data
  • Getting VEnCodes
    • Objects for generating and ranking VEnCodes

Module for VEnCode-related projects based on FANTOM5 databases

This module contains classes and functions that perform intersectional genetics-related operations to find VEnCodes using any matrix of cell types (columns) vs regulatory elements or markers (rows).

Moreover, it contains particular methods to make use of the databases provided by the FANTOM5 consortium, namely the CAGE enhancer and transcription start site (TSS) databases.

For more information on the VEnCode technology, please refer to Macedo and Gontijo, GigaScience, 2020.

Indices and tables

• Index

• Module Index

• Search Page